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Starting July 1, riders who have been taking weekend trips on the Massachusetts Bay Transportation Authority’s Greenbush and Kingston/Plymouth rail lines will have to find new ways to travel.

Wait times for the Red Line trolley from Dorchester’s Ashmont Station to Milton and Mattapan will be considerably longer on Sunday and much of Saturday. On weekends, the ferry from Quincy to Boston won’t leave the dock.

And on almost all modes of public transportation in Greater Boston, rides will be significantly more expensive.

The MBTA’s board of directors last week approved fare increases, as well as reduced service on bus, commuter rail, and ferry lines and the rapid transit Green Line, in order to close a $160 million budget gap for next fiscal year. South of Boston, cuts included elimination of weekend service on the Fore River Shipyard ferry in Quincy, the Greenbush and Kingston/Plymouth branches of the Old Colony Railroad, the Needham commuter rail line, and the 245 bus, which runs from Mattapan through Milton to Quincy Center.

The weekday 217 bus, which runs from Ashmont Station in Dorchester to Quincy Center via East Milton Square, will no longer go to Wollaston Beach. The Ashmont-to-Mattapan trolleys will run every 23 to 26 minutes - instead of the now 11 to 13 minutes - on Sundays, and before 10 a.m. and after 8 p.m. Saturdays.

The fare increase systemwide averages 23 percent. A subway rider using a Charlie Card will see the fare increase from $1.70 to $2, while bus fares will increase from $1.25 to $1.50. A one-way trip on the Hingham commuter boat will increase from $6 to $8, while commuter rail fares will increase by about 29 percent. Parking fees also will go up at some locations.

Although the T’s actions have drawn raucous protests in Boston from public transportation advocates, including activists in the Occupy Boston movement, objections have been muted south of Boston.

Braintree Mayor Joseph C. Sullivan said, “We all recognize that the MBTA has serious budget problems, but I was disappointed with the elimination of commuter rail on weekends. On the South Shore we fought hard for restoration of commuter rail and this sends the wrong message.’’

Ferry service

Martha Bewick of Hingham, a longtime advocate for the commuter boats, said she was troubled about the fare increases but pleased the service will continue.

“We are very, very happy that at least the boats will be kept,’’ Bewick said. “They were threatened with beheading.’’

The MBTA’s original plans, announced in January, called for elimination of the Hingham ferry service, as well as more than a dozen bus routes, plus fare increases of up to 43 percent. The agency instead will tap one-time revenue sources and money left in snow-removal accounts, thanks to the mild winter, to close the budget gap.

“The plan isn’t ideal, but it is a major improvement over the original proposals,’’ said state Representative Mark Cusack, a Braintree Democrat and a member of the Legislature’s Joint Transportation Committee.

The $2 fare increase for the commuter boats, coupled with a $1 increase for parking at the Hingham terminal, could put the service out of reach for many commuters, Bewick said, adding, “It’s hard to understand why the ferries are being given a double whack.’’

She also said ending the weekend ferry service from Quincy will hurt people who use the boats to visit Boston and the harbor islands in the summer.

State Senator Robert L. Hedlund, a Weymouth Republican and member of the Legislature’s Transportation Committee, called the commuter boat increases “more evidence that they have never been concerned about a healthy ferry system.’’

Hedlund noted that while the MBTA is moving to eliminate subsidies for the privately owned Hingham boats, the agency provides extensive support for commuter rail and other forms of public transit.

Commuter rail

No service cuts are planned on three area commuter rail lines - Providence/Stoughton, Franklin, and Middleborough/Lakeville. Riders on those lines, though, will have to absorb some of the biggest fare increases in the package approved by the T’s board last week.

The fare for a one-way trip from Mansfield to Boston will go from $6.75 to $8.75, while the cost of a ride from downtown Brockton to Boston will jump from $5.75 to $7.25.

“A lot of people who work in Boston choose to live in Brockton because it’s affordable,’’ said the Brockton City Council’s president, Thomas G. Brophy, who rides the train daily to Boston. “This will affect them very severely.’’

The fare hikes will hurt many people throughout Greater Boston and reduce ridership, according to John Walkey, an organizer for Transportation for Massachusetts, a coalition of planning, transportation, housing, public health, and environmental groups.

“For people on low incomes or who are transit dependent, this is going to have a drastic effect,’’ Walkey said.

Limiting harm

MBTA officials said the agency has done its best to limit harm to riders.

Officials also noted that every other major transit agency in the country has raised fares in the past five years. The T’s last fare increase was in 2007.

In a joint letter to riders issued when the changes were announced, the MBTA’s acting general manager, Jonathan Davis, and state Transportation Secretary Richard A. Davey wrote, “We understand that even these moderate changes we are proposing today will have a significant impact on some of our customers, and we appreciate that. But we have an obligation to balance our books, and to be honest with each of you about the cost of service.’’

In the letter, Davis and Davey noted that the MBTA’s financial troubles are not over, and that the agency will face another significant budget gap next year.

Public transportation advocates have begun calling for Beacon Hill to provide new taxes or other revenue sources for the T.

“The Legislature needs to step up and do its part,’’ said Marc Draisen, executive director of the Metropolitan Area Planning Council. “The riders have done their part.’’